AFAIR:
1. MIDI over MADI makes it possible to remote control devices connected to the MADI bus, not the UFX+ itself.
The UFX+ is being controlled by TM FX.
2. UFX+ in stand-alone mode can only control a few more general parameters of a MADI channel,
but it's not comparable with remote control capability of "TM FX AUX Device" or "RME MIDI Remote".

2 possibilities / general use cases for Remote Control using "MIDI over MADI" (to control other MADI devices connected to UFX+):
a) Integration of Octamic XTC as so called "AUX device"
b) Remote control by the separate software RME MIDI Remote

The advantage of Aux device: the most important XTCs settings (gain, panorama, phantom Power, PAD, Instr.) can be remote controlled inside of the TM FX instance of your UFX+. The settings can be stored digitally in an TM FX snapshot.
This is very comfortably. As of today only the XTC can be integrated as Aux Device into TM FX.

If you use "AUX Device" on one MADI channel then you can not run RME MIDI remote application anymore on the same MADI bus or there will be race conditions between MIDI remote and AUX Device comands.

To your other question. Its required that all MADI channels work to make MIDI remote possible, as MIDI remote uses unused bits of the MADI protocol. USB2 would offer to few channels, so all this can only run with USB3.

Section 28.6 of the manual, p 88:

"28.6 Stand-Alone MIDI Control
When not connected to a computer, the Fireface UFX+ can be controlled directly via MIDI.
..
the most important functions to control the Fireface UFX+, are implemented in hardware, thus available also in stand-alone mode."

The available functions are explained in that chapter, and nowhere does it say MIDI over MADI.